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Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

da Silva JM, Giachetto PF, da Silva LO, Cintra LC, Paiva SR, Caetano AR, Yamagishi ME - PLoS ONE (2015)

Bottom Line: High density genotyping panels have been used in a wide range of applications.From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data.Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

View Article: PubMed Central - PubMed

Affiliation: Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Nova Xavantina, Mato Grosso, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular-Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil.

ABSTRACT
High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

No MeSH data available.


IGV screenshot image.The double vertical lines indicate the BovineHD0500032585 SNP position. Colored positions indicate flanking SNPs. There are 6 non-synonymous SNPs and 1 synonymous SNP (4th column from left).
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pone.0136035.g009: IGV screenshot image.The double vertical lines indicate the BovineHD0500032585 SNP position. Colored positions indicate flanking SNPs. There are 6 non-synonymous SNPs and 1 synonymous SNP (4th column from left).

Mentions: Major histocompatibility complex (MHC) class I- (MR1) and class II-related genes (BOLA-DRB3, BOLA-DQA1, BOLA-DQA2), which are central to immunity and are among the most polymorphic genes known [34], were also found. Other SFNB-containing genes involved in the immune system that were identified include T-cell receptors, a TCR-α chain (which reacts with antigenic protein peptides in the context of self major histocompatibility complex (MHC) proteins), and a TCR-γ chain (which reacts with proteins that do not involve MHC presentation) [35], and CD6, a T-cell surface protein that regulates antigen-specific responses through cell-cell contact [36]. Considering the 8,737 SNPs identified in SFNB flanking regions annotated with VEP, 32 SNPs out of the 74 SNPs that were found to be located within exons resulted in non-synonymous substitutions (Table 1). An extreme case of non-synonymous mutation is shown in Fig 9. In the flanking regions of the BovineHD0500032585 SNP, there are 7 interspecies mutations, 6 of which are non-synonymous and only 1 of which is synonymous. The BovineHD0500032585 SNP is located on BTA5 at position 112,843,452 bp within an exon of EP300 (Table 1). According to Gayther et al. [37], EP300 regulates transcription through chromatin remodeling and plays a major role in cell proliferation and differentiation processes. Furthermore, in cattle, this gene has been associated with lipid metabolism [38], which is important in beef cattle meat quality. Another extreme case of non-synonymous mutations was observed in the flanking regions of BovineHD0100043813: there are 4 non-synonymous SNPs within an exon of the RIPPLY3 gene. The literature on this gene is scarce, but a recent study has shown that it is a repressor of the Tbx1 gene, which plays a major role in morphogenesis. It is also required for the development of the pharyngeal apparatus in mice [39], which is essential for eating and respiration.


Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

da Silva JM, Giachetto PF, da Silva LO, Cintra LC, Paiva SR, Caetano AR, Yamagishi ME - PLoS ONE (2015)

IGV screenshot image.The double vertical lines indicate the BovineHD0500032585 SNP position. Colored positions indicate flanking SNPs. There are 6 non-synonymous SNPs and 1 synonymous SNP (4th column from left).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4549312&req=5

pone.0136035.g009: IGV screenshot image.The double vertical lines indicate the BovineHD0500032585 SNP position. Colored positions indicate flanking SNPs. There are 6 non-synonymous SNPs and 1 synonymous SNP (4th column from left).
Mentions: Major histocompatibility complex (MHC) class I- (MR1) and class II-related genes (BOLA-DRB3, BOLA-DQA1, BOLA-DQA2), which are central to immunity and are among the most polymorphic genes known [34], were also found. Other SFNB-containing genes involved in the immune system that were identified include T-cell receptors, a TCR-α chain (which reacts with antigenic protein peptides in the context of self major histocompatibility complex (MHC) proteins), and a TCR-γ chain (which reacts with proteins that do not involve MHC presentation) [35], and CD6, a T-cell surface protein that regulates antigen-specific responses through cell-cell contact [36]. Considering the 8,737 SNPs identified in SFNB flanking regions annotated with VEP, 32 SNPs out of the 74 SNPs that were found to be located within exons resulted in non-synonymous substitutions (Table 1). An extreme case of non-synonymous mutation is shown in Fig 9. In the flanking regions of the BovineHD0500032585 SNP, there are 7 interspecies mutations, 6 of which are non-synonymous and only 1 of which is synonymous. The BovineHD0500032585 SNP is located on BTA5 at position 112,843,452 bp within an exon of EP300 (Table 1). According to Gayther et al. [37], EP300 regulates transcription through chromatin remodeling and plays a major role in cell proliferation and differentiation processes. Furthermore, in cattle, this gene has been associated with lipid metabolism [38], which is important in beef cattle meat quality. Another extreme case of non-synonymous mutations was observed in the flanking regions of BovineHD0100043813: there are 4 non-synonymous SNPs within an exon of the RIPPLY3 gene. The literature on this gene is scarce, but a recent study has shown that it is a repressor of the Tbx1 gene, which plays a major role in morphogenesis. It is also required for the development of the pharyngeal apparatus in mice [39], which is essential for eating and respiration.

Bottom Line: High density genotyping panels have been used in a wide range of applications.From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data.Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

View Article: PubMed Central - PubMed

Affiliation: Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Nova Xavantina, Mato Grosso, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular-Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil.

ABSTRACT
High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

No MeSH data available.